Thursday, October 24, 2013

In order to understand the concept of electronegativity, it is necessary to
take into account the following idea... The molecules are highly dynamic, and
electrons are in constant motion around the atoms, representing the so-called
"electron cloud". The movement of electrons around an atoms is
directly conditioned by its characteristics. That is, if an atom has a greater
ability to take over the electronic cloud, the electrons will be located
predominantly on him. Electronegativity concerns exactly with this capability.
Therefore, the more electronegative an atom is, the greater the portion of the
electron cloud on it. Consequently, the more electronegative atoms tend to have
negative partial charges, because at every moment there will be more electrons
on them than on other atoms .

It is this
asymmetry that is created in the distribution of the electron cloud that causes
the molecules to become polar. Thus, in general , the presence of different
atoms with different electronegativities in a molecule causes the molecule
becomes polar, or at least the region where this happens to become polar .

In the case of
biochemistry , since carbon and hydrogen have similar electronegativities, the
regions of the molecules that contain only these two atoms are nonpolar , while
the presence of oxygen, nitrogen , fluorine , phosphorus , etc., tend to render
that region polar .

Wednesday, October 16, 2013

What do you think about the idea to listen Frank Sinatra singing about biochemistry? Well, it is not the real Frank Sinatra that sings, but Dr. Ahern has adapted the famous song My Way and made another music about the study of biochemistry. It is for sure one of my favourite songs of Dr. Ahern! :)

Saturday, September 21, 2013

As mentioned in my first post about the non-covalent bonds , they are something
essential in biochemistry!

At one side, since they are weak forces, they allow dynamic communications
between molecules or within the same molecule. In other words, since they are
weak they may allow, for example, that two molecules interact temporarily with
one another, or that certain macromolecules acquire specific conformations
temporarily . But in either case, if you need to change this situation, it is
not complicated as these are weak forces... Examples of the first situation are
an interaction between a substrate and the active site of an enzyme (please
note that in some cases the substrate can interact with the enzyme
covalently!), an interaction between a receptor and its ligand, an interaction
between two proteins , etc. . Examples of the latter are an enzymatic
conformational changes induced by binding of a substrate or by binding of an
allosteric modulator, a protein conformational changes in response to a pH
change (which happens, for example, with phosphofructokinase -1 during lactic fermentation,
and this is one of the factors associated with muscle fatigue...), etc.

But do not be fooled by the individual weakness of each non-covalent
interaction. In fact, as in biochemistry we often deal with large molecules
(polysaccharides, proteins, nucleic acids , for example) , there are numerous
locations within those molecules that can interact with each other. Thus, they
form a network of non-covalent interactions that is responsible for maintaining
the 3D structure of these molecules. The sum of all forces becomes huge, giving
a greater stability to biomolecules. This is why, for example, a protein
acquires one or a few possible conformations, despite virtually there is an
enormous number of protein conformations that could be present...
Finally, there is a very important aspect that is related to non-covalent
forces that molecules may be involved with: its solubility! In fact, often when
someone dissolves something in water (salt or sugar, for example), does not
think on why the dissolution occured. The idea is quite simple... for a
substance to dissolve in a particular solvent, the molecules that compose it
must be able to interact with the molecules of the solvent, in an energetically
way more favorable than their initial arrangement . For example, the sum of the
network of interactions between the atoms of Na+ and Cl-
in the salt is less than the sum of the interactions of such ions with water
molecules. Thus, in the presence of water the salt dissolves. And the reasoning
is valid for any solute and/or solvent. Therefore it is said that "Like
dissolves like" , which in reality tells us that the dissolution occurs
when there is chemical affinity between the molecules of solute and solvent .

There must be a way to jam into my head - 350
All the metabolic enzyme names I dread - 350
Can you help me learn the spaces
Where the endonucleases
Cut the DNA in places 3-5-0 -350

I must find a way to make a better grade
Or my GPA will truly get waylaid
I shall overcome frustration
To achieve my aspiration
On the last examination 3-5-0, 350

Here’s the plan I made to help me to succeed
Fill the notecard with the knowledge I will need
I’ve put all of Ahern’s quotes
Along with what each one denotes
Onto a massive stack of notes for 3-5-0, 350

So there’s just one teensy problem I must fix
It requires some very skillful penman tricks
Squeezing info I must store
Onto the card he gave before
Will mean a font the size of zero point one four

Tuesday, September 3, 2013

Today
I willdedicate a postto a type ofweak interactionsthat is oftenoverlooked inchemistry classes(probably because they are weaker thancovalent bonds...), butin biochemistryareequally or moreimportant than thecovalent bonds. I'mtalking
about thenon-covalent interactions(orbonds).
Before starting totalk about them,it should be highlighted the differencebetweennon-covalent and covalent bonds. In the
firstthere is nosharing ofelectronsbetween the atomsparticipatingin the bond, while in the second type there issharing of the electrons(bonding electrons).
Because there is nosharing ofelectrons, the resulting bondis significantlyweaker.

Tuesday, June 25, 2013

As it seems obvious, Dr. Ahern made a music about the exams of Biochemistry, and about the hard work that is to study for them. He got inspiration in the song The Yellow Rose of Texas. And by the way... for all that are at this moment studying Biochemistry... Good luck! ;)

The term is almost at an endTen weeks since it beganI worried how my grade was ‘causeI did not have a planThe first exam went not so wellI got a fifty three‘Twas just about the average scoreIn Biochemistry

I buckled down the second timeDid not sow my wild oatsI downloaded the videosAnd took a ton of notesI learned about free energyAnd Delta Gee Naught PrimeMy score increased by seven pointsA C-plus grade was mine

I sang the songs, I memorizedI played the mp3sI learned the citrate cycleAnd I counted ATPsI had electron transport downAnd all of complex veeI gasped when I saw my examIt was a ninety three

So heading to the final stretchI crammed my memoryAnd came to class on sunny daysFor quizzing comedyI packed a card with info andMy brain almost burned out‘Twas much to my delight IGot the ‘A’ I’d dreamed about

So here’s the moral of the songIt doesn’t pay to stewIf scores are not quite what you wantAnd you don’t have a clueThe answers get into your headWhen you know what to doWatch videos, read highlights andReview, review, review
.

Sunday, April 21, 2013

Today I will dedicate a post to some general considerations about cellular respiration. This process occurs in the mitochondria More precisely, in the mitochondrial inner membrane. To put it in a simple way, it is an oxidation-reduction process that involves the transport of electrons, from NADH and FADH2 to oxygen. In fact, it is mainly because of this process that we need to breathe oxygen. During the process, the O2 molecules are reduced to H2O, which is the main reason for us to breathe out water vapor. Thus, in fact most of our pulmonary respiration is not more than a consequence of our cellular respiration!

But back to the cellular respiration process... The electrons are received and transported over four complexes, designated I, II, III and IV. These complexes are not more than sets of electron transport proteins, many of which with cofactors specialized in the transport of electrons, such as iron-sulfur centers, heme and flavoproteins. A key element in this process is the presence of transition metals (iron and copper, for example) because, due to the fact that they can oscillate between two oxidation states, they are able to temporarily capture or donate electrons.

For electrons to pass from complex I or II to complex III, there is a lipophilic molecule that will carry them, which is called ubiquinone. For the electrons to move from complex III to IV there is an intermembrane space protein that carries them, designated cytochrome c.

As the electrons move along the complexes, in some of them ther will be a coupled process, which is the proton (H +) pumping from the matrix to the intermembranar space. That means, it will be created a H+ gradient, designated electromotive force , which will accumulate enough energy to drive ATP synthesis via a process called oxidative phosphorylation. The intervening in this process is the mitochondrial ATP synthase.

In future posts I will devote some attention to a detailled explanation of how cellular respiration works...

Wednesday, April 17, 2013

Simon and Garfunkel have immortalized many songs, among which is the famous "The sound of silence". Dr. Ahern adapted this beautiful music and created a song about the hormone apinephrine. You can download it inwww.davincipress.com/metabmelodies.html.

The Tao of Hormones

Biochemistry my friendIt's time to study you againMechanisms that I need to knowAre the things that really stress me so"Get these pathways planted firmly in your head,"Ahern saidLet's start with ep-inephrine

Membrane proteins are well knownChanged on binding this hormoneRearranging selves without protestStimulating a G alpha STo go open up and displace its GDPWith GTPBecause of ep-inephrine

Active G then moves a waysStimulating ad cyclaseSo a bunch of cyclic AMPBinds to kinase and then sets it freeAll the active sites of the kinases awaitTriphosphateBecause of ep-inephrine

Muscles are affected thenBreaking down their glycogenSo they get a wad of energyIn the form of lots of G-1-PAnd the synthases that could make a glucose chainAll refrainBecause of ep-inephrine

Now I've reached the pathway endGoing from adrenalinHere's a trick I learned to get it rightLinking memory to flight or frightSo the mechanism that's the source of anxious fearsReappearsWhen I make ep-inephrine

Tuesday, April 2, 2013

The Krebs cycle plays a central role in our metabolism. In all the classes I give about metabolism, the Krebs cycle is present...
As I mentioned in previous posts, this process is composed by 8 steps, 3 of which are catalyzed by regulatory enzymes. These enzymes are citrate synthase (1st reaction), isocitrate dehydrogenase (3rd Reaction) and alpha-ketoglutarate dehydrogenase (4th reaction).
In this post I will talk a little about the main activators and inhibitors of each. As you will see, there are many modulators that are common to more than one enzyme, which makes life easier for those who have to study this metabolic pathway. :)

Citrate synthase:

Inhibitors
Succinyl-CoA - it is an intermediate of Krebs cycle. More specifically, it is the 4th intermediate of Krebs cycle, that means, it is formed in a reaction after the reaction that we are considering. So if we have an accumulation of intermediates formed in further reactions, it makes sense that these may inhibit the initial reactions of the pathway in question, in this case the first.
Citrate - it is the product of the reaction, so it makes sense that it might inhibit its own synthesis.
ATP - the Krebs cycle is a catabolic pathway, ie, its main goal is to produce energy (ATP). If the cell already has energy, the process is inhibited.
NADH - The reasoning is equivalent to that made for the ATP. That is, the NADH has a high energy potential, since in cellular respiration it can lead to the production of ATP, therefore it is logical that NADH functions as an inhibitor of Krebs cycle.
Long Chain fatty acid-CoA - it is not completely understood the inhibitory role of the long chain fatty acids in the Krebs cycle, but it is believed that this property is related to the fact that they behave as detergents because they are amphipathic compounds consisting of one polar part (carboxylic group) and one part apolar part (hydrocarbon chain). Oleic acid (18 carbons and one double bond at carbon 9) appears to be the major fatty acid inhibitor of citate synthase.

Activators
ADP - ADP signals an energy deficit in the cell because it is produced when ATP is spent for energy. So it makes sense that it activates the Krebs cycle, because the main objective of this pathway is the production of energy.

Isocitrate dehydrogenase:

Inhibitors
Succinyl-CoA - the reasoning that was made for the citrate synthase applies in this situation.
ATP - the reasoning that was made for the citrate synthase applies in this situation.
NADH - the reasoning that was made for the citrate synthase applies in this situation.

Activators
ADP - the reasoning that was made for the citrate synthase applies in this situation.
Ca2 + (muscle) - as I mentioned in a previous post, about the regulation of pyruvate dehydrogenase complex, Ca2+ is an intracellular messenger whose concentration increases during muscle contraction. Therefore, in this context contracting cells will require energy, so catabolic processes and, in particular, the Krebs cycle, is activated.

Alpha-ketoglutarate dehydrogenase:

Inhibitors
Succinyl-CoA - it is the product of the reaction so, it makes sense that this molecule may inhibit its own synthesis.
ATP - the reasoning that was made for the citrate synthase applies in this situation.
NADH - the reasoning that was made for the citrate synthase applies in this situation.

Activators
Ca2 + (muscle) - the reasoning that was made for isocitrate dehydrogenase applies in this situation.